Contacts of the strand formed by residues 30 - 39 (chain D) in PDB entry 4EMG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 30 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D LYS* 3.4 11.4 - - - +
26D LEU* 3.0 54.0 + - + +
27D ARG 4.5 5.6 + - - +
28D GLY 3.2 10.9 + - - +
29D ASP* 1.3 80.5 - - - +
31D GLU* 1.3 67.2 + - - +
32D LEU* 4.9 0.4 - - + -
52D GLU* 2.6 49.0 + - + +
53D ILE 3.7 2.2 - - - +
54D VAL* 3.4 25.5 - - + +
25G LYS* 3.1 38.9 - - - +
28G GLY 5.6 1.8 - - - +
29G ASP 5.5 0.6 - - - +
86G ILE* 4.8 14.2 - - - +
87G LEU* 4.6 8.5 - - - -
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Residues in contact with GLU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C LYS* 4.2 11.3 - - - +
23D TYR* 2.7 42.1 + - + +
24D VAL 3.3 6.3 - - - +
25D LYS* 4.0 10.3 - - + +
26D LEU 4.7 0.2 - - - +
29D ASP 5.7 0.2 - - - -
30D ARG* 1.3 79.9 - - - +
32D LEU* 1.3 73.8 + - - +
33D ASN* 5.4 0.4 - - - +
52D GLU* 4.0 0.5 - - - +
53D ILE* 2.9 52.6 + - + +
55D THR* 4.0 21.2 - - + +
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Residues in contact with LEU 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D VAL 4.5 0.4 - - - -
23D TYR* 3.5 3.6 - - - -
24D VAL* 2.8 36.9 + - + +
26D LEU* 3.9 23.1 - - + -
30D ARG* 4.9 0.9 - - + -
31D GLU* 1.3 83.7 - - - +
33D ASN* 1.3 72.7 + - - +
47D LEU* 3.9 18.8 - - + -
51D GLU 3.2 4.9 - - - +
52D GLU* 3.6 28.7 - - + -
78D LEU* 3.9 16.4 - - + -
80D VAL* 3.5 42.2 - - + -
87G LEU* 4.4 4.9 - - + -
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Residues in contact with ASN 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ILE* 5.0 9.0 - - + +
22D VAL 3.3 7.7 - - - +
23D TYR* 3.8 26.8 - - - +
31D GLU* 5.3 1.0 - - - +
32D LEU* 1.3 80.7 + - - +
34D GLY* 1.3 59.1 + - - +
47D LEU* 4.7 2.9 - - - -
49D ASP 4.0 1.1 - - - +
50D ALA* 3.1 4.9 - - - +
51D GLU* 2.8 55.5 + - + +
53D ILE* 4.0 16.6 - - - +
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Residues in contact with GLY 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ILE* 3.2 11.9 - - - +
22D VAL* 2.8 33.6 + - - +
33D ASN* 1.3 75.4 - - - +
35D ARG* 1.3 62.2 + - - -
36D LEU 3.6 0.9 + - - -
47D LEU* 4.0 16.3 - - - +
48D GLY 3.5 9.6 - - - -
49D ASP 4.0 5.4 - - - -
50D ALA* 4.1 1.3 - - - -
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Residues in contact with ARG 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ASP* 3.0 47.9 + - - +
20D GLU* 3.4 5.8 - - - +
21D ILE* 3.8 32.2 - - + +
34D GLY* 1.3 70.6 - - - -
36D LEU* 1.3 59.8 - - - +
37D HIS* 3.1 33.9 + - + +
47D LEU* 3.3 2.8 - - - -
48D GLY 2.7 41.2 + - - +
49D ASP* 5.6 4.7 - - + +
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Residues in contact with LEU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D VAL* 3.4 38.8 - - + +
17D SER* 3.6 26.5 - - - +
18D LEU* 3.7 14.8 - - + +
19D ASP* 2.7 31.0 + - - -
20D GLU 3.0 10.9 + - - +
22D VAL* 4.2 13.7 - - + -
34D GLY 3.6 2.6 + - - -
35D ARG* 1.3 68.8 - - - +
37D HIS* 1.3 59.8 + - - +
38D ALA 3.5 25.1 - - - +
39D TYR* 4.4 1.6 - - + -
45D MSE 3.8 24.0 - - + -
46D VAL 3.9 1.8 - - - +
47D LEU* 4.0 13.7 - - + -
88D ILE* 6.0 1.1 - - + -
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Residues in contact with HIS 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 3.9 10.1 - - - +
19D ASP* 4.2 21.0 + - - +
35D ARG* 3.1 27.7 + - + -
36D LEU* 1.3 74.1 - - - +
38D ALA* 1.3 64.5 + - + +
46D VAL* 3.0 20.9 + - + +
48D GLY* 3.6 35.7 + - - -
77D MSE 3.7 23.4 - - + -
9G GLU* 4.9 3.3 - - - +
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Residues in contact with ALA 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 4.1 6.8 - - - +
36D LEU* 3.5 7.1 - - - +
37D HIS* 1.3 83.5 - - + +
39D TYR* 1.3 64.6 + - - +
45D MSE 3.2 4.5 - - - -
46D VAL* 2.9 32.2 + - + -
9G GLU* 3.4 32.1 - - + +
10G PRO* 3.9 17.3 - - + -
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Residues in contact with TYR 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 4.7 13.3 + - + +
14D VAL* 3.7 26.5 - - + -
15D ARG* 3.1 43.2 - - - +
18D LEU* 3.6 34.9 - - + +
36D LEU* 4.4 4.0 - - + -
38D ALA* 1.3 78.8 - - - +
40D ASP* 1.3 77.6 + - - +
43D LEU* 5.0 5.2 - - + -
44D ASN 3.0 13.2 - - - +
45D MSE 3.9 13.0 - - + -
9G GLU* 5.0 2.3 - - - +
10G PRO* 3.4 10.8 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il